MRI_Convert_Opera_To_Hyperstack
The tool converts images taken with the Opera into hyperstacks. The image names are in the form
r02c04f01p01-ch1sk1fk1fl1.tiff
where r is the row, c the column, f the field, p the z-position and ch the channel. The tool converts all images in the input folder. You can find an example image here: image.zip. Download and unzip it and run the tool on the image folder.
Please find the source code in github here.
To install the tool, download the files Convert_Opera_To_Hyperstack.ijm and convert_Opera_To_Hyperstack.py, save them into the folder macros/toolsets of your FIJI installation and restart FIJI.
Select the "Convert Opera to Hyperstack" toolset from the >> button of the ImageJ launcher.
Right-click the co-button to open the options dialog:
- saturated - value used to adjust the display via the ImageJ command "Enhance Contrast".
- output folder - the name of the subfolder of the input folder into which the result images will be written
Click the co-button to run the script. A file dialog will be opened. Select the folder with the input images. The result images will be written into a subfolder of the input folder.
Volker Bäcker